same problem here with ST2 2217 and OS X 10.7.5
Everything worked perfecty until yesterday evening.
This morning the sidebar stopped to autorefresh.
Nothing changed in the project settings, nor do I have symlinked files. The problem affects the whole project tree.
I can use the sidebar to delete files and to create new ones... and they ARE created and deleted correctly. Still, it doesn't update.
Same story if I create or remove a file using the terminal (either through a script or manually). It doesn't update.
It had always updated automatically... until today I didn't even know about the "project->refresh folders" menu option.
I tried to empty the application cache files and preferences, but to no result.